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- PDB-5hu3: Drosophila CaMKII-D136N in complex with a phosphorylated fragment... -

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Basic information

Entry
Database: PDB / ID: 5hu3
TitleDrosophila CaMKII-D136N in complex with a phosphorylated fragment of the Eag potassium channel and Mg2+/ADP
Components
  • Calcium/calmodulin-dependent protein kinase type II alpha chain
  • Potassium voltage-gated channel protein eag
KeywordsTRANSFERASE / protein kinase / potassium channel / complex
Function / homology
Function and homology information


perineurial glial growth / regulation of ovulation / Ca2+ pathway / Ion transport by P-type ATPases / HSF1-dependent transactivation / RAF activation / Ion homeostasis / positive regulation of synaptic transmission, dopaminergic / Unblocking of NMDA receptors, glutamate binding and activation / behavioral response to ether ...perineurial glial growth / regulation of ovulation / Ca2+ pathway / Ion transport by P-type ATPases / HSF1-dependent transactivation / RAF activation / Ion homeostasis / positive regulation of synaptic transmission, dopaminergic / Unblocking of NMDA receptors, glutamate binding and activation / behavioral response to ether / Voltage gated Potassium channels / courtship behavior / regulation of synaptic assembly at neuromuscular junction / male courtship behavior / Ca2+/calmodulin-dependent protein kinase / regulation of filopodium assembly / voltage-gated monoatomic cation channel activity / calcium/calmodulin-dependent protein kinase activity / negative regulation of cytokine production / regulation of heart contraction / neuromuscular junction development / presynaptic active zone / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / voltage-gated potassium channel activity / long-term memory / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to starvation / regulation of membrane potential / learning / potassium ion transport / sensory perception of smell / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / learning or memory / calmodulin binding / neuron projection / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage-dependent, EAG / : / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain ...Potassium channel, voltage-dependent, EAG / : / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / NTF2-like domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Calcium/calmodulin-dependent protein kinase type II alpha chain / Potassium voltage-gated channel protein eag
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.885 Å
AuthorsCastro-Rodrigues, A.F. / Morais-Cabral, J.H.
CitationJournal: J.Mol.Biol. / Year: 2018
Title: The Interaction between the Drosophila EAG Potassium Channel and the Protein Kinase CaMKII Involves an Extensive Interface at the Active Site of the Kinase.
Authors: Castro-Rodrigues, A.F. / Zhao, Y. / Fonseca, F. / Gabant, G. / Cadene, M. / Robertson, G.A. / Morais-Cabral, J.H.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase type II alpha chain
B: Potassium voltage-gated channel protein eag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1214
Polymers37,6702
Non-polymers4522
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-31 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.907, 59.217, 70.301
Angle α, β, γ (deg.)90.000, 96.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type II alpha chain / CaM-kinase II alpha chain


Mass: 32180.680 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-283 / Mutation: D136N
Source method: isolated from a genetically manipulated source
Details: Constitutively active CaMKII kinase domain construct
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CaMKII, CaM, CG18069 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q00168, Ca2+/calmodulin-dependent protein kinase
#2: Protein Potassium voltage-gated channel protein eag / Ether-a-go-go protein


Mass: 5488.898 Da / Num. of mol.: 1 / Fragment: UNP Residues 768-820
Source method: isolated from a genetically manipulated source
Details: Eag construct including the CaMKII-binding motif / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: eag, CG10952 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02280
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 19% PEG 4000, 0.1 M sodium citrate pH 5.0, 0.2 M ammonium acetate, 5 mM magnesium chloride, 0.8 mM ADP
PH range: 5.0 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.82→30.075 Å / Num. all: 26540 / Num. obs: 26540 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 31.38 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.041 / Rsym value: 0.034 / Net I/av σ(I): 15.324 / Net I/σ(I): 19.3 / Num. measured all: 87981
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.82-1.882.40.5721.4585424120.4550.7360.5721.591
1.88-1.9530.4791.6739224760.3310.5850.4792.697.3
1.95-2.033.50.3282.4857024370.2060.3880.328499.2
2.03-2.133.40.2233.5801823380.1420.2650.2236.299.3
2.13-2.233.50.1495.2788522430.0930.1760.1498.199.6
2.23-2.353.40.1027.6706120950.0670.1220.1021297.2
2.35-2.493.50.07510.3716820470.0470.0890.07514.599.7
2.49-2.663.50.05314.2664618950.0330.0620.0531999.6
2.66-2.883.50.03719.8624817970.0230.0440.03725.699.9
2.88-3.153.50.02724.2570816230.0170.0320.0273599.7
3.15-3.523.40.02426514314920.0150.0280.02443.299.5
3.52-4.073.40.02128.9437412970.0130.0250.02151.598.9
4.07-4.983.30.02129.7369811140.0130.0250.02156.198.9
4.98-7.053.40.01637.829458710.010.0190.01655.699.3
7.05-30.0753.20.01442.712714030.0090.0170.01457.681.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.885→30.075 Å / FOM work R set: 0.7364 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1211 5.04 %
Rwork0.1918 22823 -
obs0.1936 24034 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.44 Å2 / Biso mean: 48.66 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.885→30.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 28 79 2364
Biso mean--39.13 41.4 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172376
X-RAY DIFFRACTIONf_angle_d1.3473241
X-RAY DIFFRACTIONf_chiral_restr0.081348
X-RAY DIFFRACTIONf_plane_restr0.007414
X-RAY DIFFRACTIONf_dihedral_angle_d16.628878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.885-1.96050.42011260.39742462258896
1.9605-2.04970.35281320.27712560269299
2.0497-2.15770.31761310.28352517264899
2.1577-2.29280.30351320.25482511264397
2.2928-2.46980.22991300.213725592689100
2.4698-2.71820.24971460.209625332679100
2.7182-3.11120.20321460.189325732719100
3.1112-3.91840.21161320.16692574270699
3.9184-30.07830.18261360.14512534267096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.885-0.00020.50425.16510.13225.35430.0219-0.1962-0.07290.587-0.3379-0.18820.04760.11230.22410.169-0.05050.03170.33290.04110.31711.88059.5317-6.3974
21.87870.8567-0.64014.78420.20065.2232-0.12860.11160.0388-1.3099-0.20530.5514-0.2218-0.53610.21580.45140.0641-0.12150.3007-0.05160.3368-4.642413.1823-26.2282
34.4333-0.3829-1.09879.63193.88337.32550.082-0.42580.0259-0.4274-0.1316-0.9392-0.82490.6240.04470.3094-0.06440.00160.33650.13060.36056.065117.9011-20.3317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 130 )A7 - 130
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 272 )A131 - 272
3X-RAY DIFFRACTION3chain 'B' and (resid 780 through 795 )B780 - 795

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